On a fast calculation of structure factors at a subatomic resolution
Identifieur interne : 002000 ( Istex/Corpus ); précédent : 001F99; suivant : 002001On a fast calculation of structure factors at a subatomic resolution
Auteurs : P. V. Afonine ; A. UrzhumtsevSource :
- Acta Crystallographica Section A [ 0108-7673 ] ; 2004-01.
English descriptors
- Teeft :
- Accurate calculation, Acta, Acta cryst, Additional displacement factor, Additional displacement parameter badd, Afonine, Agarwal, Aldose, Aldose reductase, Aldose reductase model, Algorithm, Anisotropic, Anisotropy, Atomic displacement parameter, Atomic displacement parameters, Atomic model, Atomic radii, Atomic radius, Badd, Badd rtotal, Beff, Calculation, Computational, Computational cost, Computational errors, Crambin, Crambin model, Cryst, Crystallographic criterion, Density distribution, Density generation, Different types, Direct formula, Direct formulae, Displacement factors, Displacement parameter, Effective radius, Electron density, Eyck, Eyck algorithm, Fourier, Grid, Grid density values, Grid points, Grid step, High accuracy, High resolution, Intermediate generation, Isotropic atoms, Kgrid, Lunin, Lunin urzhumtsev, Macromolecular, Macromolecular crystals, Macromolecular models, Matrix, Matrix ucart, Maximal grid step, Minimal value, Navaza, Normal matrix, Optimal choice, Optimal value, Other hand, Parameter, Podjarny, Protein crystallography, Radius, Ras, Reductase, Relative accuracy, Relative error, Research papers, Research papers table, Resolution zones, Same time, Small molecules, Space group, Structure factor, Structure factors, Subatomic, Subatomic resolution, Tfft ttotal tform tformattotal, Total number, Ttotal, Ucart, Unit cell, Urzhumtsev.
Abstract
In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9 Å. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high‐quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for `small‐molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re‐examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). Acta Cryst.4, 362–367; Ten Eyck (1977). Acta Cryst. A33, 486–492] may be much more computationally efficient, but contains some parameters (grid step, `effective' atom radii etc.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct‐formulae calculations. The impact of the different parameters on the computer efficiency of structure‐factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested.
Url:
DOI: 10.1107/S0108767303022062
Links to Exploration step
ISTEX:8A31F42E2DD31EE06A48CEC0E77B28255AE930FDLe document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">On a fast calculation of structure factors at a subatomic resolution</title><author><name sortKey="Afonine, P V" sort="Afonine, P V" uniqKey="Afonine P" first="P. V." last="Afonine">P. V. Afonine</name></author><author><name sortKey="Urzhumtsev, A" sort="Urzhumtsev, A" uniqKey="Urzhumtsev A" first="A." last="Urzhumtsev">A. Urzhumtsev</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:8A31F42E2DD31EE06A48CEC0E77B28255AE930FD</idno><date when="2004" year="2004">2004</date><idno type="doi">10.1107/S0108767303022062</idno><idno type="url">https://api.istex.fr/ark:/67375/WNG-SWVNZK97-0/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">002000</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">002000</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">On a fast calculation of structure factors at a subatomic resolution</title><author><name sortKey="Afonine, P V" sort="Afonine, P V" uniqKey="Afonine P" first="P. V." last="Afonine">P. V. Afonine</name></author><author><name sortKey="Urzhumtsev, A" sort="Urzhumtsev, A" uniqKey="Urzhumtsev A" first="A." last="Urzhumtsev">A. Urzhumtsev</name></author></analytic><monogr></monogr><series><title level="j" type="main">Acta Crystallographica Section A</title><title level="j" type="alt">ACTA CRYSTALLOGRAPHICA A</title><idno type="ISSN">0108-7673</idno><idno type="eISSN">1600-5724</idno><imprint><biblScope unit="vol">60</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="19">19</biblScope><biblScope unit="page" to="32">32</biblScope><publisher>Munksgaard International Publishers</publisher><pubPlace>5 Abbey Square, Chester, Cheshire CH1 2HU, England</pubPlace><date type="published" when="2004-01">2004-01</date></imprint><idno type="ISSN">0108-7673</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0108-7673</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Accurate calculation</term><term>Acta</term><term>Acta cryst</term><term>Additional displacement factor</term><term>Additional displacement parameter badd</term><term>Afonine</term><term>Agarwal</term><term>Aldose</term><term>Aldose reductase</term><term>Aldose reductase model</term><term>Algorithm</term><term>Anisotropic</term><term>Anisotropy</term><term>Atomic displacement parameter</term><term>Atomic displacement parameters</term><term>Atomic model</term><term>Atomic radii</term><term>Atomic radius</term><term>Badd</term><term>Badd rtotal</term><term>Beff</term><term>Calculation</term><term>Computational</term><term>Computational cost</term><term>Computational errors</term><term>Crambin</term><term>Crambin model</term><term>Cryst</term><term>Crystallographic criterion</term><term>Density distribution</term><term>Density generation</term><term>Different types</term><term>Direct formula</term><term>Direct formulae</term><term>Displacement factors</term><term>Displacement parameter</term><term>Effective radius</term><term>Electron density</term><term>Eyck</term><term>Eyck algorithm</term><term>Fourier</term><term>Grid</term><term>Grid density values</term><term>Grid points</term><term>Grid step</term><term>High accuracy</term><term>High resolution</term><term>Intermediate generation</term><term>Isotropic atoms</term><term>Kgrid</term><term>Lunin</term><term>Lunin urzhumtsev</term><term>Macromolecular</term><term>Macromolecular crystals</term><term>Macromolecular models</term><term>Matrix</term><term>Matrix ucart</term><term>Maximal grid step</term><term>Minimal value</term><term>Navaza</term><term>Normal matrix</term><term>Optimal choice</term><term>Optimal value</term><term>Other hand</term><term>Parameter</term><term>Podjarny</term><term>Protein crystallography</term><term>Radius</term><term>Ras</term><term>Reductase</term><term>Relative accuracy</term><term>Relative error</term><term>Research papers</term><term>Research papers table</term><term>Resolution zones</term><term>Same time</term><term>Small molecules</term><term>Space group</term><term>Structure factor</term><term>Structure factors</term><term>Subatomic</term><term>Subatomic resolution</term><term>Tfft ttotal tform tformattotal</term><term>Total number</term><term>Ttotal</term><term>Ucart</term><term>Unit cell</term><term>Urzhumtsev</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract">In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9 Å. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high‐quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for `small‐molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re‐examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). Acta Cryst.4, 362–367; Ten Eyck (1977). Acta Cryst. A33, 486–492] may be much more computationally efficient, but contains some parameters (grid step, `effective' atom radii etc.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct‐formulae calculations. The impact of the different parameters on the computer efficiency of structure‐factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested.</div></front></TEI><istex><corpusName>wiley</corpusName><keywords><teeft><json:string>structure factors</json:string><json:string>grid</json:string><json:string>cryst</json:string><json:string>acta</json:string><json:string>urzhumtsev</json:string><json:string>acta cryst</json:string><json:string>grid step</json:string><json:string>lunin</json:string><json:string>badd</json:string><json:string>beff</json:string><json:string>eyck</json:string><json:string>electron density</json:string><json:string>atomic radius</json:string><json:string>afonine</json:string><json:string>anisotropic</json:string><json:string>fourier</json:string><json:string>density generation</json:string><json:string>atomic radii</json:string><json:string>subatomic resolution</json:string><json:string>aldose</json:string><json:string>ucart</json:string><json:string>navaza</json:string><json:string>crambin</json:string><json:string>kgrid</json:string><json:string>algorithm</json:string><json:string>reductase</json:string><json:string>unit cell</json:string><json:string>ttotal</json:string><json:string>grid points</json:string><json:string>relative accuracy</json:string><json:string>agarwal</json:string><json:string>displacement parameter</json:string><json:string>subatomic</json:string><json:string>direct formulae</json:string><json:string>matrix</json:string><json:string>atomic displacement parameter</json:string><json:string>ras</json:string><json:string>aldose reductase</json:string><json:string>podjarny</json:string><json:string>parameter</json:string><json:string>atomic model</json:string><json:string>lunin urzhumtsev</json:string><json:string>research papers</json:string><json:string>intermediate generation</json:string><json:string>structure factor</json:string><json:string>computational</json:string><json:string>space group</json:string><json:string>atomic displacement parameters</json:string><json:string>eyck algorithm</json:string><json:string>isotropic atoms</json:string><json:string>radius</json:string><json:string>accurate calculation</json:string><json:string>minimal value</json:string><json:string>high resolution</json:string><json:string>optimal value</json:string><json:string>grid density values</json:string><json:string>high accuracy</json:string><json:string>resolution zones</json:string><json:string>relative error</json:string><json:string>maximal grid step</json:string><json:string>displacement factors</json:string><json:string>optimal choice</json:string><json:string>matrix ucart</json:string><json:string>macromolecular models</json:string><json:string>small molecules</json:string><json:string>additional displacement parameter badd</json:string><json:string>other hand</json:string><json:string>anisotropy</json:string><json:string>macromolecular</json:string><json:string>computational cost</json:string><json:string>research papers table</json:string><json:string>different types</json:string><json:string>density distribution</json:string><json:string>computational errors</json:string><json:string>protein crystallography</json:string><json:string>crystallographic criterion</json:string><json:string>additional displacement factor</json:string><json:string>effective radius</json:string><json:string>macromolecular crystals</json:string><json:string>crambin model</json:string><json:string>aldose reductase model</json:string><json:string>direct formula</json:string><json:string>total number</json:string><json:string>normal matrix</json:string><json:string>badd rtotal</json:string><json:string>tfft ttotal tform tformattotal</json:string><json:string>same time</json:string><json:string>calculation</json:string></teeft></keywords><author><json:item><name>P. V. Afonine</name></json:item><json:item><name>A. Urzhumtsev</name></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>structure factors</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>CPU optimization</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>electron‐density generation</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>fast algorithms.</value></json:item></subject><articleId><json:string>AYAGC0047</json:string></articleId><arkIstex>ark:/67375/WNG-SWVNZK97-0</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>miscellaneous</json:string></originalGenre><abstract>In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9 Å. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high‐quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for `small‐molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re‐examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). Acta Cryst.4, 362–367; Ten Eyck (1977). Acta Cryst. A33, 486–492] may be much more computationally efficient, but contains some parameters (grid step, `effective' atom radii etc.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct‐formulae calculations. The impact of the different parameters on the computer efficiency of structure‐factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested.</abstract><qualityIndicators><score>10</score><pdfWordCount>10476</pdfWordCount><pdfCharCount>59322</pdfCharCount><pdfVersion>1.1</pdfVersion><pdfPageCount>14</pdfPageCount><pdfPageSize>610 x 794 pts</pdfPageSize><refBibsNative>false</refBibsNative><abstractWordCount>307</abstractWordCount><abstractCharCount>2104</abstractCharCount><keywordCount>4</keywordCount></qualityIndicators><title>On a fast calculation of structure factors at a subatomic resolution</title><genre><json:string>article</json:string></genre><host><title>Acta Crystallographica Section A</title><language><json:string>unknown</json:string></language><doi><json:string>10.1111/(ISSN)1600-5724</json:string></doi><issn><json:string>0108-7673</json:string></issn><eissn><json:string>1600-5724</json:string></eissn><publisherId><json:string>AYA</json:string></publisherId><volume>60</volume><issue>1</issue><pages><first>19</first><last>32</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date></date><geogName></geogName><orgName></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName></persName><placeName></placeName><ref_url></ref_url><ref_bibl></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/WNG-SWVNZK97-0</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - crystallography</json:string></wos><scienceMetrix><json:string>1 - natural sciences</json:string><json:string>2 - chemistry</json:string><json:string>3 - inorganic & nuclear chemistry</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Structural Biology</json:string></scopus></categories><publicationDate>2004</publicationDate><copyrightDate>2004</copyrightDate><doi><json:string>10.1107/S0108767303022062</json:string></doi><id>8A31F42E2DD31EE06A48CEC0E77B28255AE930FD</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-SWVNZK97-0/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-SWVNZK97-0/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/WNG-SWVNZK97-0/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main">On a fast calculation of structure factors at a subatomic resolution</title><respStmt><resp>Références bibliographiques récupérées via GROBID</resp><name resp="ISTEX-API">ISTEX-API (INIST-CNRS)</name></respStmt></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Munksgaard International Publishers</publisher><pubPlace>5 Abbey Square, Chester, Cheshire CH1 2HU, England</pubPlace><date type="published" when="2004-01"></date></publicationStmt><notesStmt><note type="content-type" subtype="other" source="miscellaneous" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-7474895G-0">other</note><note type="publication-type" subtype="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="other"><analytic><title level="a" type="main">On a fast calculation of structure factors at a subatomic resolution</title><title level="a" type="short">Fast calculation of structure factors</title><author xml:id="author-0000"><persName><forename type="first">P. V.</forename><surname>Afonine</surname></persName><affiliation>
LCMB, UMR 7036 CNRS, Faculté des Sciences, BP 239, Université Henri Poincaré, Nancy 1, Vandoeuvre‐lès‐Nancy 54506, FranceCentre Charles Hermite, LORIA, Villers‐lès‐Nancy 54602, France<address><country key="FR FR"></country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">A.</forename><surname>Urzhumtsev</surname></persName><affiliation>
LCMB, UMR 7036 CNRS, Faculté des Sciences, BP 239, Université Henri Poincaré, Nancy 1, Vandoeuvre‐lès‐Nancy 54506, FranceCentre Charles Hermite, LORIA, Villers‐lès‐Nancy 54602, France<address><country key="FR FR"></country></address></affiliation></author><idno type="istex">8A31F42E2DD31EE06A48CEC0E77B28255AE930FD</idno><idno type="ark">ark:/67375/WNG-SWVNZK97-0</idno><idno type="DOI">10.1107/S0108767303022062</idno><idno type="unit">AYAGC0047</idno><idno type="society">gc0047</idno><idno type="toTypesetVersion">file:AYA.AYAgc0047.pdf</idno></analytic><monogr><title level="j" type="main">Acta Crystallographica Section A</title><title level="j" type="alt">ACTA CRYSTALLOGRAPHICA A</title><idno type="pISSN">0108-7673</idno><idno type="eISSN">1600-5724</idno><idno type="book-DOI">10.1111/(ISSN)1600-5724</idno><idno type="book-part-DOI">10.1111/aya.2004.60.issue-1</idno><idno type="product">AYA</idno><imprint><biblScope unit="vol">60</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="19">19</biblScope><biblScope unit="page" to="32">32</biblScope><publisher>Munksgaard International Publishers</publisher><pubPlace>5 Abbey Square, Chester, Cheshire CH1 2HU, England</pubPlace><date type="published" when="2004-01"></date></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><abstract xml:lang="en" style="main"><p>In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9 Å. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high‐quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for `small‐molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re‐examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). <hi rend="italic">Acta Cryst.</hi><hi rend="italic">4</hi>, 362–367; Ten Eyck (1977). <hi rend="italic">Acta Cryst.</hi> A<hi rend="italic">33</hi>, 486–492] may be much more computationally efficient, but contains some parameters (grid step, `effective' atom radii <hi rend="italic">etc</hi>.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct‐formulae calculations. The impact of the different parameters on the computer efficiency of structure‐factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested.</p></abstract><textClass><keywords xml:lang="en"><term xml:id="k1">structure factors</term><term xml:id="k2">CPU optimization</term><term xml:id="k3">electron‐density generation</term><term xml:id="k4">fast algorithms.</term></keywords><keywords rend="tocHeading1"><term>research papers</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change xml:id="refBibs-istex" who="#ISTEX-API" when="2018-06-14">References added</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-SWVNZK97-0/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Munksgaard International Publishers</publisherName><publisherLoc>5 Abbey Square, Chester, Cheshire CH1 2HU, England</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1600-5724</doi><issn type="print">0108-7673</issn><issn type="electronic">1600-5724</issn><idGroup><id type="product" value="AYA"></id></idGroup><titleGroup><title type="main" sort="ACTA CRYSTALLOGRAPHICA A">Acta Crystallographica Section A</title><title type="short">Acta Cryst. A</title></titleGroup></publicationMeta><publicationMeta level="part" position="01001"><doi origin="wiley">10.1111/aya.2004.60.issue-1</doi><numberingGroup><numbering type="journalVolume" number="60">60</numbering><numbering type="journalIssue" number="1">1</numbering></numberingGroup><coverDate startDate="2004-01">January 2004</coverDate></publicationMeta><publicationMeta level="unit" type="miscellaneous" position="0001900" status="forIssue"><doi origin="wiley">10.1107/S0108767303022062</doi><idGroup><id type="unit" value="AYAGC0047"></id><id type="society" value="gc0047"></id></idGroup><titleGroup><title type="tocHeading1">research papers</title></titleGroup><eventGroup><event type="firstOnline" date="2004-03-11"></event><event type="publishedOnlineFinalForm" date="2004-03-11"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.3.2 mode:FullText source:FullText result:FullText" date="2010-02-27"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-06"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-14"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="19">19</numbering><numbering type="pageLast" number="32">32</numbering></numberingGroup><correspondenceTo>A. Urzhumtsev, LCM3B, UMR 7036 CNRS, Faculté des Sciences, BP 239, Université Henri Poincaré, Nancy 1, Vandoeuvre‐lès‐Nancy 54506, France. E‐mail: <email normalForm="alexander.ourjoumtsev@lcm3b.uhp-nancy.fr">alexander.ourjoumtsev@lcm3b.uhp‐nancy.fr</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:AYA.AYAgc0047.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 1 August 2003, accepted 3 October 2003</unparsedEditorialHistory><countGroup><count type="figureTotal" number="9"></count><count type="tableTotal" number="4"></count><count type="formulaTotal" number="25"></count><count type="wordTotal" number="13375"></count><count type="referenceTotal" number="43"></count><count type="linksCrossRef" number="10"></count><count type="linksPubMed" number="7"></count></countGroup><titleGroup><title type="main">On a fast calculation of structure factors at a subatomic resolution</title><title type="shortAuthors">Afonine and Urzhumtsev</title><title type="short">Fast calculation of structure factors</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1"><personName><givenNames>P. V.</givenNames><familyName>Afonine</familyName></personName></creator><creator creatorRole="author" xml:id="cr2"><personName><givenNames>A.</givenNames><familyName>Urzhumtsev</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="FR"><unparsedAffiliation>
LCM<sup>3</sup>B, UMR 7036 CNRS, Faculté des Sciences, BP 239, Université Henri Poincaré, Nancy 1, Vandoeuvre‐lès‐Nancy 54506, France</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="FR"><unparsedAffiliation>Centre Charles Hermite, LORIA, Villers‐lès‐Nancy 54602, France</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">structure factors</keyword><keyword xml:id="k2">CPU optimization</keyword><keyword xml:id="k3">electron‐density generation</keyword><keyword xml:id="k4">fast algorithms.</keyword></keywordGroup><abstractGroup><abstract type="main" xml:lang="en"><p>In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9 Å. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high‐quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for `small‐molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re‐examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). <i>Acta Cryst.</i><b>4</b>, 362–367; Ten Eyck (1977). <i>Acta Cryst.</i> A<b>33</b>, 486–492] may be much more computationally efficient, but contains some parameters (grid step, `effective' atom radii <i>etc</i>.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct‐formulae calculations. The impact of the different parameters on the computer efficiency of structure‐factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>On a fast calculation of structure factors at a subatomic resolution</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Fast calculation of structure factors</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>On a fast calculation of structure factors at a subatomic resolution</title></titleInfo><name type="personal"><namePart type="given">P. V.</namePart><namePart type="family">Afonine</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A.</namePart><namePart type="family">Urzhumtsev</namePart><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="miscellaneous" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Munksgaard International Publishers</publisher><place><placeTerm type="text">5 Abbey Square, Chester, Cheshire CH1 2HU, England</placeTerm></place><dateIssued encoding="w3cdtf">2004-01</dateIssued><edition>Received 1 August 2003, accepted 3 October 2003</edition><copyrightDate encoding="w3cdtf">2004</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><extent unit="figures">9</extent><extent unit="tables">4</extent><extent unit="formulas">25</extent><extent unit="references">43</extent><extent unit="linksCrossRef">10</extent><extent unit="words">13375</extent></physicalDescription><abstract>In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9 Å. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high‐quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for `small‐molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re‐examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). Acta Cryst.4, 362–367; Ten Eyck (1977). Acta Cryst. A33, 486–492] may be much more computationally efficient, but contains some parameters (grid step, `effective' atom radii etc.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct‐formulae calculations. The impact of the different parameters on the computer efficiency of structure‐factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested.</abstract><subject lang="en"><genre>keywords</genre><topic>structure factors</topic><topic>CPU optimization</topic><topic>electron‐density generation</topic><topic>fast algorithms.</topic></subject><relatedItem type="host"><titleInfo><title>Acta Crystallographica Section A</title></titleInfo><titleInfo type="abbreviated"><title>Acta Cryst. A</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><identifier type="ISSN">0108-7673</identifier><identifier type="eISSN">1600-5724</identifier><identifier type="DOI">10.1111/(ISSN)1600-5724</identifier><identifier type="PublisherID">AYA</identifier><part><date>2004</date><detail type="volume"><caption>vol.</caption><number>60</number></detail><detail type="issue"><caption>no.</caption><number>1</number></detail><extent unit="pages"><start>19</start><end>32</end></extent></part></relatedItem><identifier type="istex">8A31F42E2DD31EE06A48CEC0E77B28255AE930FD</identifier><identifier type="ark">ark:/67375/WNG-SWVNZK97-0</identifier><identifier type="DOI">10.1107/S0108767303022062</identifier><identifier type="ArticleID">AYAGC0047</identifier><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-L0C46X92-X">wiley</recordContentSource><recordOrigin>Munksgaard International Publishers</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-SWVNZK97-0/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Lorraine/explor/InforLorV4/Data/Istex/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002000 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Istex/Corpus/biblio.hfd -nk 002000 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Lorraine
|area= InforLorV4
|flux= Istex
|étape= Corpus
|type= RBID
|clé= ISTEX:8A31F42E2DD31EE06A48CEC0E77B28255AE930FD
|texte= On a fast calculation of structure factors at a subatomic resolution
}}
| This area was generated with Dilib version V0.6.33. |  |